exons & protein domains
gjb at bioch.ox.ac.uk
Wed Jul 31 08:10:04 EST 1996
Andrew J. Roger wrote:
> Gary DosSantos wrote:
> > This is off the topic, but I was wondering if any algorithms have been
> > written that allow for the generation of phylogenetic trees by aligning
> > structural domains. A typical protein does not have all that many
> > structural domains, certainly not enough to perform a bootstrap
> > analysis. It seems to me then, that by using structural domains as a
> > criteria for protein alignment, one could not obtain the amount of data
> > necessary for estimating the degree of relatedness between groups of
> > proteins, but could only say that such and such proteins are related.
> Look in the last chapter of Methods in Enzymology, Volume 183. There
> is a paper using three dimensional structure to construct
> evolutionary trees (it is a distance method, I believe).
Yes. That is a good start, but there has been a lot of work done
over the last 5 years on the subject of comparing protein 3D structures
using a variety of different measures of similarity or distance.
Look at the work of Taylor and Orengo and Sali and Blundell and Holm
and Sander for a start.
Although similarities of protein three dimensional structure are often
used to infer that the two proteins have a common ancestor. On
its own, structural similarity is rarely enough to confirm homology.
For an intriguing example from my own work see Russell and Barton
(1993), Nature, 364, 765.
Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of
Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K.
mailto:gjb at bioch.ox.ac.uk, Tel: +44 1865 275368, Fax: +44 1865 510454,
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